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The youthful boy cries out as his head is forcefully gripped, a large thumb pressing into his cheek as his father's mighty palm holds him by the throat. This moment from Abraham's Sacrifice visits the Florentine museum, creating distress through Caravaggio's chilling rendition of the tormented child from the biblical narrative. The painting appears as if the patriarch, instructed by God to kill his offspring, could break his spinal column with a single turn. Yet Abraham's chosen approach involves the metallic grey blade he holds in his remaining palm, ready to slit Isaac's neck. One certain aspect remains – whomever posed as Isaac for this breathtaking work demonstrated extraordinary acting skill. There exists not just dread, shock and begging in his shadowed eyes but also profound sorrow that a protector could abandon him so completely.

The artist took a familiar scriptural story and transformed it so fresh and raw that its terrors appeared to unfold directly in view of you

Viewing in front of the artwork, observers recognize this as a real countenance, an precise depiction of a young model, because the same youth – identifiable by his tousled locks and almost black pupils – features in several other paintings by the master. In every case, that richly emotional visage commands the scene. In Youth With a Ram, he peers playfully from the shadows while embracing a lamb. In Amor Vincit Omnia, he smirks with a hardness learned on Rome's streets, his black feathery wings demonic, a unclothed adolescent creating riot in a affluent dwelling.

Victorious Cupid, presently displayed at a London museum, represents one of the most embarrassing artworks ever created. Observers feel totally disoriented gazing at it. The god of love, whose arrows fill people with often agonizing desire, is portrayed as a extremely real, vividly illuminated unclothed form, straddling overturned objects that comprise stringed devices, a musical score, plate armour and an architect's T-square. This pile of possessions resembles, intentionally, the mathematical and construction equipment strewn across the ground in the German master's print Melencolia I – save in this case, the gloomy disorder is caused by this grinning Cupid and the turmoil he can release.

"Affection looks not with the eyes, but with the mind, / And therefore is winged Love depicted sightless," wrote Shakespeare, just before this work was created around 1601. But the painter's Cupid is not blind. He gazes straight at you. That face – sardonic and ruddy-cheeked, staring with bold assurance as he poses unclothed – is the identical one that screams in fear in Abraham's Test.

When the Italian master painted his three portrayals of the same unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the most acclaimed religious painter in a metropolis enflamed by religious revival. Abraham's Offering demonstrates why he was sought to adorn churches: he could adopt a scriptural story that had been depicted numerous occasions before and render it so new, so raw and visceral that the horror appeared to be happening directly before the spectator.

However there was a different aspect to the artist, evident as soon as he arrived in Rome in the cold season that concluded the sixteenth century, as a painter in his early 20s with no mentor or supporter in the urban center, only talent and boldness. Most of the paintings with which he captured the sacred metropolis's attention were anything but holy. What could be the absolute earliest hangs in the UK's art museum. A young man opens his red mouth in a scream of agony: while reaching out his dirty fingers for a cherry, he has instead been bitten. Boy Bitten By a Lizard is sensuality amid poverty: viewers can see the painter's dismal room reflected in the murky waters of the transparent vase.

The adolescent wears a pink flower in his coiffure – a symbol of the sex trade in early modern art. Northern Italian artists such as Titian and Palma Vecchio portrayed prostitutes grasping flowers and, in a work lost in the second world war but known through photographs, Caravaggio represented a famous woman courtesan, clutching a posy to her bosom. The meaning of all these botanical signifiers is obvious: sex for sale.

What are we to interpret of Caravaggio's erotic depictions of youths – and of one boy in specific? It is a inquiry that has divided his commentators ever since he achieved widespread recognition in the twentieth century. The complex past reality is that the artist was neither the homosexual hero that, for example, the filmmaker presented on film in his 1986 film Caravaggio, nor so entirely devout that, as certain art scholars unbelievably claim, his Youth Holding Fruit is actually a portrait of Jesus.

His early paintings do offer explicit sexual implications, or even offers. It's as if the painter, then a penniless young creator, identified with Rome's prostitutes, selling himself to survive. In the Uffizi, with this idea in consideration, observers might turn to an additional early work, the sixteenth-century masterwork Bacchus, in which the deity of wine gazes calmly at the spectator as he starts to untie the black sash of his garment.

A few annums following Bacchus, what could have driven Caravaggio to paint Victorious Cupid for the artistic collector Vincenzo Giustiniani, when he was finally growing almost established with prestigious ecclesiastical projects? This profane pagan god resurrects the sexual challenges of his initial works but in a increasingly intense, unsettling way. Fifty years afterwards, its hidden meaning seemed obvious: it was a portrait of Caravaggio's companion. A English traveller viewed Victorious Cupid in about the mid-seventeenth century and was told its subject has "the body & face of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this boy was Francesco.

The artist had been deceased for about forty annums when this story was recorded.